title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-2

status: Public on Aug 31 2008

city: Newark

first: David

middle: M.

last: Lukac

state: NJ

address: 225 Warren St.; ICPH E350C; PO Box 1709

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers Univ./NJ Medical School

hyb_protocol: Microcon 10 columns (YM 10; Millipore) were primed with 400 uL 1x TE buffer (Tris-EDTA pH 8.0) by centrifugation at RT for 10 min. Paired Cy3-labeled and Cy5-labeled cDNAs were combined, added to the primed column, and purified by centrifugation. When approximately 25 uL of liquid remained above the membrane, an extra 200 uL 1x TE buffer was added to wash the column.  Centrifugation was continued until approximately 4.5 uL liquid remained above the membrane. The purified, labeled cDNAs were transferred to a new tube and combined with an equal volume of hybridization mixture (0.5 uL 10mg/ml tRNA (Sigma), 0.5 uL 10mg/ml salmon sperm DNA (Sigma), 1.0 uL 20x SSC, 2.5 uL formamide (Fisher), and 1.0 uL 1% SDS). The mixture was heated for 2 min at 98°C, and cooled for 5 min at RT immediately before loading on the microarray slides.       Prior to hybridization, the slides were blocked in pre-hybridization solution (3.0 g bovine serum albumin [fraction V; Roche], 1.2ml 10% SDS, 106.0 ml Milli-Q water) at 42°C for 1 h. The pre-hybridized slides were washed with nuclease-free water for 2 min, isopropanol for 2 min, and subsequently dried by centrifugation. The labeled cDNAs were applied to slides, covered by a 22 x 22-mm cover-slip (Corning), sealed in a hybridization chamber (GeneMachines), and hybridized at 50°C overnight. After hybridization, cover-slips were removed by submerging the slides in solution I (2x SSC, 1% SDS), rinsed in solution II (1x SSC, 0.05%SDS) for 1 min, and rinsed in solution III (0.06x SSC) for 2 min.

scan_protocol: Slides were dried by centrifugation and scanned immediately with a GenePix4000B scanner (Molecular Devices). The images were processed using GenePix 5.1. Data were filtered by removing all spots that were below the background noise or flagged as ‘bad’.  Spots were considered to be below the background noise if the sum of the median intensities of the two channels was less than twice the highest mean background of the chip. The chips were normalized by the print-tip Lowess method.

data_processing:
The ratio of the mean median intensity of Cy5 over the mean median intensity of Cy3 was determined for each spot.
	Dye ratios for viral genes from the same transfections that were hybridized to greater than one independent micro-array were internally normalized to the averaged dye ratios of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), then viral spots were averaged. Each viral dye ratio was normalized to that of the KSHV true late ORF25/Major capsid protein transcript (as quantitated by Northern blotting, the MCP transcript was unaffected by Rta-ER WT and mutants in presence of protein synthesis inhibitors).
The five resulting data sets were tested for significant changes in gene expression  using two methods:  Method 1. Average number of standard deviations from mean of each data set:  dye ratios of each spot for Rta_NLS1,2-ER were divided by dye ratios for ER vector to determine spot-specific effects of 4-OHT addition.  Means of the triplicate dye ratios were calculated to determine gene specific effects of 4-OHT addition.  Each data set was log transformed and fit to a normal (Gaussian) distribution, and the means of the normalized gene-specific values were calculated.  The resulting set of gene-specific means was fit to a normal distribution, outliers were excluded using Peirce’s criterion (hypothesis: one outlier per gene), and the average number of standard deviations from the mean was calculated for each gene.  Method 2. q-values: gene specific t tests and q values (chance of being false positive, expressed as a percentage) were calculated by comparing the dye ratios of each spot for Rta_NLS1,2-ER to the dye ratios for ER vector using  the software program significance analysis of microarrays (SAM).

label: cyanine 5-dUTP [Cy5]

organism:
Chlorocebus aethiops
Human gammaherpesvirus 8

label_protocol: 3 or 6 ugs. of each RNA sample (equal amounts per pair) were adjusted to 11 uL with dH2O. 2.2 ul of random hexamers (2 ug/ul; Sigma-Genosys) were added, the mixture was heated at 98°C for 2 minutes, then snapped cool on ice. 11.1 uL of master mix (5.0 uL First-strand buffer, 2.5 uL 100mM DTT, 2.3 uL low dTdNTP mix [5mM A,G,C and 0.2mM T stock], containing 1.5 uL cyanine 5-dUTP [Cy5] [PerkinElmer]) was added. The mixture was subsequently supplemented with 1.2 uL Superscript (Invitrogen), then incubated for 10 minutes at 25°C, followed by 90 min at 42°C.

growth_protocol: Vero-rKSHV.219 cells were grown in complete Dulbecco’s modified Eagle medium (DMEM) supplemented with 6ug/ml puromycin as described in Vieira and O'Hearn (Virology 325; 225-240).

extract_protocol: Extraction and purification by RNABee (Tel-test), as recommended by manufacturer.

treatment_protocol: For transfection, cells were seeded at 1x10^6 per 10-cm plate to obtain ~50 to 70% confluence the following day, and transfected with empty ER vector using TransIT-LT1 transfection reagent with 10 ug DNA according to the manufacturer’s (Mirus) instructions. Hygromycin B (300 ug/mL; Invitrogen) was added to cultures 3 hours post-transfection, and 4-hydroxytamoxifen (4-OHT; 0.1 mM; Sigma), was added 15 hours post-hygromycin.  Total RNA was harvested 15 hours following 4-OHT addition.

tag: Vero-rKSHV.219 cells are Vero cells infected with recombinant Human herpesvirus-8/Kaposi's sarcoma-associated herpesvirus.

label: cyanine 3-dUTP [Cy3]

label_protocol: 3 or 6 ugs. of each RNA sample (equal amounts per pair) were adjusted to 11 uL with dH2O. 2.2 ul of random hexamers (2 ug/ul; Sigma-Genosys) were added, the mixture was heated at 98°C for 2 minutes, then snapped cool on ice. 11.1 uL of master mix (5.0 uL First-strand buffer, 2.5 uL 100mM DTT, 2.3 uL low dTdNTP mix [5mM A,G,C and 0.2mM T stock], containing 1.5 uL cyanine 3-dUTP [Cy3] [PerkinElmer]) was added. The mixture was subsequently supplemented with 1.2 uL Superscript (Invitrogen), then incubated for 10 minutes at 25°C, followed by 90 min at 42°C.

treatment_protocol: For transfection, cells were seeded at 1x10^6 per 10-cm plate to obtain ~50 to 70% confluence the following day, and transfected with empty ER vector using TransIT-LT1 transfection reagent with 10 ug DNA according to the manufacturer’s (Mirus) instructions. Hygromycin B (300 ug/mL; Invitrogen) was added to cultures 3 hours post-transfection.  Total RNA was harvested 30 hours following hygromycin addition.


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-3

type: RNA

country: USA

molecule: total RNA


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-2


title: ESC dcr (Illumina)

status: Public on Sep 10 2008

city: San Francisco

first: James

middle: Graham

last: Ruby

state: CA

address: 1700 4th Street QB3 s404

department: Biochemistry

institute: UCSF

data_processing: Small RNA sequences 16-27 nt long are provided with the number of reads for each unique sequence.  Small RNA 5p ends were observed as the 5p end of the Illumina read.  Small RNA 3p ends were determined using matches to ligated linker sequences.

organism: Mus musculus

source_name: dcr(-) ES cells

growth_protocol: Mouse embryonic stem cells were grown on gelatin-coated plates in standard, feeder-free conditions, using MEF conditioned media as previously described (Wang et al. 2007). DGCR8 knockout ES cells were previously described (Wang et al. 2007).  Dicer knockout cells were produced by first deriving ES cells  (Blelloch et al. 2006) from Dicer flox/flox mice (kindly provided to us by Michael McManus - (Harfe et al. 2005)). Resulting cells were treated with cre recombinase to loop out the floxed Dicer alleles.  Homozygous loop out was confirmed by genotyping (Harfe et al. 2005).

extract_protocol: Total RNA from wt, dgcr8Δ/Δ and dicer1Δ/Δ was extracted using Trizol (Invitrogen). Small RNA libraries were constructed essentially as previously described (Lau et al. 2001). Small RNAs ranging from 18 to 32 nucleotides were gel purified and ligated to the 3´ adaptor and 5´ adaptor oligonucleotides. Products from the second ligation were purified, reverse transcribed, and amplified using corresponding primers. Sequences of the adaptors and primers are as published (Illumina, 454 Life Sciences). Samples were sequenced on an Illumina 1G Genome Analyzer and 454 Genome Sequencer.

tag: cultured embryonic stem cells


title: Skin Papilloma (Tail)_c-Fos-floxed_sample2 Cy3

status: Public on Sep 01 2008

city: Stanford

first: Daniel

last: Haag

state: Santa Clara

address: 265 Campus Drive

department: ISCBRM

institute: Stanford School of Medicine

description:
Tumor model: mice overexpressing Sos in keratinocytes leading to a constitutive activation of the Ras pathway, which results in formation of skin papilloma.
Experiment: papillomas from c-Fos fl/fl mice (harboring active c-Fos) are compared to papillomas from c-Fos Δ/ Δ mice (lacking c-Fos)

hyb_protocol: Purified, dye-labelled cDNA was mixed with 120 μl UltraHyb hybridization buffer (Ambion), agitated for 30–60 min at 60°C, then for 10 min at 70°C on a thermo mixer and subsequently applied to pre-heated (60°C) microarrays mounted in a GeneTAC Hybridization Station (Genomic Solutions, Ann Arbor). Hybridizations were performed for 23 h at 42°C with gentle agitation. Thereafter, the arrays were automatically washed at 36°C with (i) 0.5× SSC, 0.1% (w/v) SDS for 5 min; (ii) 0.05× SSC, 0.1% (w/v) SDS for 3 min; and (iii) 0.05× SSC for 2 min. Flow time was set to 40 s. Immediately after the completion of the final washing step, the arrays were unmounted, immersed in 0.05× SSC, 0.1% (w/v) Tween 20 and dried by centrifugation in 50 ml Falcon tubes (30 s at 500, 1000 and 1500 r.p.m., respectively, followed by a final step of 240 s at 2000 r.p.m.).

scan_protocol: Hybridized microarrays were scanned in a two-color Agilent Scanner G25505B (Agilent, Santa Clara, CA) at 5 μm resolution and automatically adjusting PMT voltages according to manufactures specification.  Recorded images were subsequently analyzed using GenePix Pro 6.0 software.

data_processing: Data tables of raw intensity values were filtered excluding those features that were either user-flagged, exhibited a foreground intensity mean-to-median ration of more than 0.3 fold change difference or having an overall foreground intensity of below 250. For normalization of filtered features, the variance stabilization normalization algorithm (Huber et al., 2002) was applied. The “VALUE”-column contains the Log-ratio in sample over reference orientation for the respective microarray.

source_name: mouse skin papilloma, c-Fos-floxed, SOS+

label_protocol:
For reverse transcription:
RNA/primer-mix: 2 µg total RNA, 500 ng (dT)-T7 primer, total volume 6 µl
; denature RNA/primer 4' at 70°C, chill on ice;

RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl

; add ice cold RT-mix, mix well
; incubate 1h at 50°C with heated lid, inactivate 15' at 65°C, chill on ice;
For second strand synthesis:
SSS-mix: 15 µl 5x 2nd strand buffer (Invitrogen), 1.5 µl 10 mM dNTP-mix, 2.22 µl DNA Pol. I (9 U/µl) (Promega), 0.1 µl RNase H (10 U/µl) (Epicentre), 0.5 µl DNA Ligase (10 U/µl) (USB), 45.68 µl RNase-free water, total volume 65 µl
; add ice cold SSS-mix to RT reaction, mix well
; incubate 2h at 14-16°C in thermal cycler
; add 3.33 µl T4 DNA-Pol. (3 U/µl) (NEB) , mix by flicking
; incubate 15' at 14-16°C in thermal cycler, heat inactivate 10' at 70°C
; add 75 µl phenol/chlorof./isoamylalc. (pH 8), mix vigorously by pipetting
; transfer to prespun (30'' at 16000g) PLG Heavy 0.5 ml (Eppendorf)
; spin 5' at 16000g
; transfer aq. phase to prepared (resuspend, drain by gravity, 2' at 1000g) P-6 MicroSpin column (BioRad)
; spin 4' at 1000g, recover eluate
; transfer eluate to 0.5 ml PCR tube
; add LPA, 3.5 µl 5 M NaCl, 220 µl 100% Ethanol, mix well
; precipitate 60' at -80°C over night
; spin tube 30' at 16000g, 4°C, remove supernatant
; wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000g, remove supernatant
; resuspend dried cDNA-pellet in 10 µl water

For In Vitro transcription:
IVT-mix (Promega): 6 µl RNase free water, 8 µl 5x T7 Transcr. buffer, 3 µl each 100 mM ATP, GTP, CTP, UTP, 4 µl T7 Enzyme-mix, total volume 30 µl
; add IVT-mix to 10 µl cDNA, mix by pipetting
; incubate 12h at 37°C
For aRNA cleanup:
RLT / β-ME – mix: 3.5 µl β-mercapto-ethanol, 76.5 µl water, 350 µl RLT (Qiagen RNeasy), total	volume 430 µl

; add RLT / β-ME-mix to IVT product (aRNA), mix well
; add 250 µl 100% ethanol, apply to RNeasy Mini column (Qiagen)
; spin 15" at 8000g, discard flow-through, transfer column to new 2 ml tube
; wash with 500 µl RPE, spin 15" at 8000g, discard flow-through
; add 30 µl RNase-free water onto membrane, spin 1' at 8000g,repeat eluting step,
; precipitate aRNA with 1 µl LPA, 30 µl 7.5M ammonium-acetate and 227.5 µl 100% ethanol
; wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000g, remove supernatant
; resuspend in RNase-free water ( 200 µg/µl)
For 2nd Round RT:
RNA/primer-mix: 5 µl aRNA (1 µg), 1 µg N6-random-primer, total volume 6 µl

; RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl

; denature RNA/primer-mix 5' at 70°C, snap cool on ice 2', hold 5' at room temperature, mix well
; incubate:
20' at 37°C
20' at 42°C
10' at 50°C
10' at 55°C
15' at 65°C
hold at 37°C
; add 1 µl RNase H-dilution (1:10 in 5x 2nd strand buffer, (Invitrogen))
; incubate 30' at 37°C, 2' at 95°C
For Klenow-labeling (per channel):
Klenow-mix (Invitrogen): 40 µl 2.5X Random Primer Solution, 10 µl 10X dNTP-(low dTTP)-mix*, 3 µl Cy-labeled dUTP (Cy3 or Cy5), 34 µl water, 2 µl Klenow fragment Exo- (40 U/µl), total volume 89 µl

;  add to cDNA (11 µl), mix gently but thoroughly
;  incubate 16h at 37°C
; add 450 µl TE to labeled cDNA, apply to Microcon YM-30 column (Millipore)
; spin 13’ at 16000g, discard flow-through
; wash with 430 µl TE (measure dye incorporation on NanoDrop), add 18.75 µl blocking-mix**,
; spin 13’ at rpm, discard flow-through
; elute labeled cDNA by inverting column into new tube, spin 8’ at 16000g

* 2 mM dATP, 2mM dCTP, 2mM dGTP, 0.5 mM dTTP
**12.5 µl Cot-1 DNA (1 µg/µl), 2.5 µl poly-A RNA (5 µg/µl), 3.75 µl tRNA (10 µg/µl)

growth_protocol:
Animals were housed in specific pathogen free (SPF) and in light, temperature and
humidity controlled conditions. Food and water were available ad libitum.

extract_protocol: Total RNA was isolated from mouse skin using TRIzol (Invitrogen) following manufacturer’s protocol. (http://www.invitrogen.com/content.cfm?pageid=469)

tag: Tissue

value: skin from tail;

tag: Tumor stage

value: papilloma;

tag: Genetic background

value: mixed 129/Ola-C57BL/6-CBA-LVA-B6C3F1

source_name: Universal Mouse Reference RNA (Stratagene)

extract_protocol: Extraction of total RNA was accomplished by (Stratagene). According to manufacturer’s specification an Absolutely RNA Kit, based on a glassfiber method in combination with guanidine thiocyanate buffer was used.

value: Liver, hepatocyte; Testis, leydig cell; Kidney; Mammary gland; Embryo; Lung, alveolar macrophage; Skin, epidermis; Thymus, T lymphocyte; Meyloma, B lymphocyte; Soleuse muscle, myoblast; Embryo, fibroblast


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-1


title: Skin Papilloma (Tail)_c-Fos-deficient_sample8 Cy5

source_name: mouse skin papilloma, c-Fos-deficient, SOS+


title: Skin Papilloma (Tail)_c-Fos-deficient_sample6 Cy5


title: Skin Papilloma (Tail)_c-Fos-floxed_sample5 Cy5


title: Skin Papilloma (Tail)_c-Fos-floxed_sample3 Cy5

label_protocol:
For reverse transcription:
RNA/primer-mix: 2 µg total RNA, 500 ng (dT)-T7 primer, total volume 6 µl
; denature RNA/primer 4' at 70°C, chill on ice;

RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl

; add ice cold RT-mix, mix well
; incubate 1h at 50°C with heated lid, inactivate 15' at 65°C, chill on ice;
For second strand synthesis:
SSS-mix: 15 µl 5x 2nd strand buffer (Invitrogen), 1.5 µl 10 mM dNTP-mix, 2.22 µl DNA Pol. I (9 U/µl) (Promega), 0.1 µl RNase H (10 U/µl) (Epicentre), 0.5 µl DNA Ligase (10 U/µl) (USB), 45.68 µl RNase-free water, total volume 65 µl
; add ice cold SSS-mix to RT reaction, mix well
; incubate 2h at 14-16°C in thermal cycler
; add 3.33 µl T4 DNA-Pol. (3 U/µl) (NEB) , mix by flicking
; incubate 15' at 14-16°C in thermal cycler, heat inactivate 10' at 70°C
; add 75 µl phenol/chlorof./isoamylalc. (pH 8), mix vigorously by pipetting
; transfer to prespun (30'' at 16000g) PLG Heavy 0.5 ml (Eppendorf)
; spin 5' at 16000g
; transfer aq. phase to prepared (resuspend, drain by gravity, 2' at 1000g) P-6 MicroSpin column (BioRad)
; spin 4' at 1000g, recover eluate
; transfer eluate to 0.5 ml PCR tube
; add LPA, 3.5 µl 5 M NaCl, 220 µl 100% Ethanol, mix well
; precipitate 60' at -80°C over night
; spin tube 30' at 16000g, 4°C, remove supernatant
; wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000g, remove supernatant
; resuspend dried cDNA-pellet in 10 µl water

For In Vitro transcription:
IVT-mix (Promega): 6 µl RNase free water, 8 µl 5x T7 Transcr. buffer, 3 µl each 100 mM ATP, GTP, CTP, UTP, 4 µl T7 Enzyme-mix, total volume 30 µl
; add IVT-mix to 10 µl cDNA, mix by pipetting
; incubate 12h at 37°C
For aRNA cleanup:
RLT / β-ME – mix: 3.5 µl β-mercapto-ethanol, 76.5 µl water, 350 µl RLT (Qiagen RNeasy), total	volume 430 µl

; add RLT / β-ME-mix to IVT product (aRNA), mix well
; add 250 µl 100% ethanol, apply to RNeasy Mini column (Qiagen)
; spin 15" at 8000g, discard flow-through, transfer column to new 2 ml tube
; wash with 500 µl RPE, spin 15" at 8000g, discard flow-through
; add 30 µl RNase-free water onto membrane, spin 1' at 8000g,repeat eluting step,
; precipitate aRNA with 1 µl LPA, 30 µl 7.5M ammonium-acetate and 227.5 µl 100% ethanol
; wash pellet with 500 µl 70% ethanol, spin tube 5' at 16000g, remove supernatant
; resuspend in RNase-free water ( 200 µg/µl)
For 2nd Round RT:
RNA/primer-mix: 5 µl aRNA (1 µg), 1 µg N6-random-primer, total volume 6 µl

; RT-mix: 2 µl M-MuLV RT buffer (Fermentas), 0.5 µl 10 mM dNTP-mix, 0.5 µl T4gp32, 0.5 µl RNase Inhibitor (Promega) , 0.5 µl reverse transcriptase (RevertAid, Fermentas), total volume 4 µl

; denature RNA/primer-mix 5' at 70°C, snap cool on ice 2', hold 5' at room temperature, mix well
; incubate:
20' at 37°C
20' at 42°C
10' at 50°C
10' at 55°C
15' at 65°C
hold at 37°C
; add 1 µl RNase H-dilution (1:10 in 5x 2nd strand buffer, (Invitrogen))
; incubate 30' at 37°C, 2' at 95°C
For Klenow-labeling (per channel):
Klenow-mix (Invitrogen): 40 µl 2.5X Random Primer Solution, 10 µl 10X dNTP-(low dTTP)-mix*, 3 µl Cy-labeled dUTP (Cy3 or Cy5), 34 µl water, 2 µl Klenow fragment Exo- (40 U/µl), total volume 89 µl

;  add to cDNA (11 µl), mix gently but thoroughly
;  incubate 16h at 37°C
; add 450 µl TE to labeled cDNA, apply to Microcon YM-30 column (Millipore)
; spin 13’ at 16000g, discard flow-through
; wash with 430 µl TE (measure dye incorporation on NanoDrop), add 18.75 µl blocking-mix**,
; spin 13’ at 16000g, discard flow-through
; elute labeled cDNA by inverting column into new tube, spin 8’ at 16000g

* 2 mM dATP, 2mM dCTP, 2mM dGTP, 0.5 mM dTTP
**12.5 µl Cot-1 DNA (1 µg/µl), 2.5 µl poly-A RNA (5 µg/µl), 3.75 µl tRNA (10 µg/µl)

tag: Gender

value: pooled

value: unknown;


title: Skin Papilloma (Tail)_c-Fos-floxed_sample5 Cy3


title: Skin Papilloma (Tail)_c-Fos-deficient_sample6 Cy3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-1


title: Skin Papilloma (Tail)_c-Fos-deficient_sample9 Cy3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-1


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-3


title: Skin Papilloma (Tail)_c-Fos-floxed_sample3 Cy3


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample5-Repl-1


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-3


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-3


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample4-Repl-1


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-1


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-3


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-1


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2B-Repl-3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2A-Repl-3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus 4-OHT-Sample2A-Repl-3

hyb_protocol: Microcon 10 columns (YM 10; Millipore) were primed with 400 uL 1x TE buffer (Tris-EDTA pH 8.0) by centrifugation at RT for 10 min. Paired Cy3-labeled and Cy5-labeled cDNAs were combined, added to the primed column, and purified by centrifugation. When approximately 25 uL of liquid remained above the membrane, an extra 200 uL 1x TE buffer was added to wash the column.  Centrifugation was continued until approximately 4.5 uL liquid remained above the membrane. The purified, labeled cDNAs were transferred to a new tube and combined with an equal volume of hybridization mixture (0.5 uL 10mg/ml tRNA (Sigma), 0.5 uL 10mg/ml salmon sperm DNA (Sigma), 1.0 uL 20x SSC, 2.5 uL formamide (Fisher), and 1.0 uL 1% SDS). The mixture was heated for 2 min at 98°C, and cooled for 5 min at RT immediately before loading on the microarray slides.        Prior to hybridization, the slides were blocked in pre-hybridization solution (3.0 g bovine serum albumin [fraction V; Roche], 1.2ml 10% SDS, 106.0 ml Milli-Q water) at 42°C for 1 h. The pre-hybridized slides were washed with nuclease-free water for 2 min, isopropanol for 2 min, and subsequently dried by centrifugation. The labeled cDNAs were applied to slides, covered by a 22 x 22-mm cover-slip (Corning), sealed in a hybridization chamber (GeneMachines), and hybridized at 50°C overnight. After hybridization, cover-slips were removed by submerging the slides in solution I (2x SSC, 1% SDS), rinsed in solution II (1x SSC, 0.05%SDS) for 1 min, and rinsed in solution III (0.06x SSC) for 2 min.

treatment_protocol: 70% confluence the following day, and transfected with RTAdeltaNLS1,2-ER vector using TransIT-LT1 transfection reagent with 10 ug DNA according to the manufacturer’s (Mirus) instructions. Hygromycin B (300 ug/mL; Invitrogen) was added to cultures 3 hours post-transfection, and 4-hydroxytamoxifen (4-OHT; 0.1 mM; Sigma), was added 15 hours post-hygromycin.  Total RNA was harvested 15 hours following 4-OHT addition.

treatment_protocol: For transfection, cells were seeded at 1x10^6 per 10-cm plate to obtain ~50 to 70% confluence the following day, and transfected with RTAdeltaNLS1,2-ER vector using TransIT-LT1 transfection reagent with 10 ug DNA according to the manufacturer’s (Mirus) instructions. Hygromycin B (300 ug/mL; Invitrogen) was added to cultures 3 hours post-transfection.  Total RNA was harvested 30 hours following hygromycin addition.


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2A-Repl-2


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2A-Repl-2


title: Skin Papilloma (Tail)_c-Fos-floxed_sample2 Cy5

source_name: Universal Mouse Reference (Stratagene), 11 pooled cell lines

value: skin from tail

value: papilloma


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2A-Repl-1


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-2

data_processing:
The ratio of the mean median intensity of Cy5 over the mean median intensity of Cy3 was determined for each spot.
	Dye ratios for viral genes from the same transfections that were hybridized to greater than one independent micro-array were internally normalized to the averaged dye ratios of glyceraldehyde 3-phosphate dehydrogenase (GAPDH), then viral spots were averaged. Each viral dye ratio was normalized to that of the KSHV true late ORF25/Major capsid protein transcript (as quantitated by Northern blotting, the MCP transcript was unaffected by Rta-ER WT and mutants in presence of protein synthesis inhibitors).
The five resulting data sets were tested for significant changes in gene expression  using two methods:  Method 1. Average number of standard deviations from mean of each data set:  dye ratios of each spot for RtaΔNLS1,2-ER were divided by dye ratios for ER vector to determine spot-specific effects of 4-OHT addition.  Means of the triplicate dye ratios were calculated to determine gene specific effects of 4-OHT addition.  Each data set was log transformed and fit to a normal (Gaussian) distribution, and the means of the normalized gene-specific values were calculated.  The resulting set of gene-specific means was fit to a normal distribution, outliers were excluded using Peirce’s criterion (hypothesis: one outlier per gene), and the average number of standard deviations from the mean was calculated for each gene.  Method 2. q-values: gene specific t tests and q values (chance of being false positive, expressed as a percentage) were calculated by comparing the dye ratios of each spot for RtaΔNLS1,2-ER to the dye ratios for ER vector using  the software program significance analysis of microarrays (SAM).

treatment_protocol: For transfection, cells were seeded at 1x10^6 per 10-cm plate to obtain ~50 to 70% confluence the following day, and transfected with RTAdeltaNLS1,2-ER vector using TransIT-LT1 transfection reagent with 10 ug DNA according to the manufacturer’s (Mirus) instructions. Hygromycin B (300 ug/mL; Invitrogen) was added to cultures 3 hours post-transfection, and 4-hydroxytamoxifen (4-OHT; 0.1 mM; Sigma), was added 15 hours post-hygromycin.  Total RNA was harvested 15 hours following 4-OHT addition.


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-3


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample3-Repl-1


title: RTAdeltaNLS1,2-ER-Transfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-1


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-3


title: 224 Day 3 siMut10 transfected biological rep3

city: Princeton

first: Fei

last: Huang

institute: Bristol-Myers Squibb Co

description: Gene expression data from cultured melanoma cancer cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized, washed and stained using the Affymetrix Fluidics Station 400 according to Affymetrix standard procedures

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

label: biotin

organism: Homo sapiens

source_name: cultured human melanoma cancer cell 224

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA isolated from cell culture using RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: NRAS-MUT10 (siMut10) transfected cells from Day 3

tag: cell line


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-2


title: 224 Day 3 siMut10 transfected biological rep1


title: ESC dgcr8 (Illumina)

source_name: dgcr8(-) ES cells


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample1-Repl-1


title: Tumor 9158

status: Public on Aug 30 2008

city: Chicago

first: yuanyuan

last: zha

state: IL

department: Department of Pathology

institute: University of Chicago

description: Gene expression data from Tumor 9158

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.Affymetrix GeneChip Scanner 3000.

data_processing: The acquisition and initial quantification of array images were performed using the GCOS (Affymetrix). Subsequent data analysis involved the normalization of array values followed by non-supervised hierarchical clustering, using dChip software.

source_name: Tumor 9158

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tumor samples were obtained by core biopsy or excisional biopsy, or were obtained form material resected from patients as part of routine clinical management.  Samples were obtained from patients who signed a written informed consent for tissue procurement clinical trials at the University of Chicago or University of Virginia.

extract_protocol: Total RNA was extracted from tumor samples (80mg each) using the GenElute Mammalian Total RNA Miniprep Kit according to the manufacturer's instructions.

treatment_protocol: Tumor was grossly separated from non-tumor tissue and a portion was quickly frozen in liquid nitrogen for preparation of RNA and for long-term storage.

tag: Metastatic melanoma biopsy


title: Tumor 12A

description: Gene expression data from Tumor 12A

source_name: Tumor 12A


title: Tumor 8326

description: Gene expression data from Tumor 8326

source_name: Tumor 8326


title: Tumor 8327

description: Gene expression data from Tumor 8327

source_name: Tumor 8327


title: Tumor 38

description: Gene expression data from Tumor 38

source_name: Tumor 38


title: Tumor 19B

description: Gene expression data from Tumor 19B

source_name: Tumor 19B


title: Tumor 85

description: Gene expression data from Tumor 85

source_name: Tumor 85


title: Tumor 1435

description: Gene expression data from Tumor 1435

source_name: Tumor 1435


title: Tumor 33

description: Gene expression data from Tumor 33

source_name: Tumor 33


title: Tumor 9156

description: Gene expression data from Tumor 9156

source_name: Tumor 9156


title: Mel MP

description: Gene expression data from Mel MP

source_name: Mel MP

tag: Mel MP


title: Tumor 35

description: Gene expression data from Tumor 35

source_name: Tumor 35


title: Tumor 6258

description: Gene expression data from Tumor 6258

source_name: Tumor 6258


title: Tumor 11A

description: Gene expression data from Tumor 11A

source_name: Tumor 11A


title: Tumor 9154

description: Gene expression data from Tumor 9154

source_name: Tumor 9154


title: Tumor 15A

description: Gene expression data from Tumor 15A

source_name: Tumor 15A


title: Tumor 843

description: Gene expression data from Tumor 843

source_name: Tumor 843


title: Tumor 13A

description: Gene expression data from Tumor 13A

source_name: Tumor 13A


title: Tumor 598

description: Gene expression data from Tumor 598

source_name: Tumor 598


title: Tumor 13B

description: Gene expression data from Tumor 13B

source_name: Tumor 13B


title: ESC wild type (Illumina)

source_name: wt ES cells


title: Tumor 4A

description: Gene expression data from Tumor 4A

source_name: Tumor 4A


title: Tumor 9295

description: Gene expression data from Tumor 9295

source_name: Tumor 9295


title: VectorTransfected-Vero-rKSHV.219cells-Hygro-Plus/Minus4-OHT-Sample2A-Repl-1

organism: Human gammaherpesvirus 8


title: Tumor 3735

description: Gene expression data from Tumor 3735

source_name: Tumor 3735


title: Tumor 1B

description: Gene expression data from Tumor 1B

source_name: Tumor 1B


title: Tumor 19A

description: Gene expression data from Tumor 19A

source_name: Tumor 19A


title: Tumor 2A

description: Gene expression data from Tumor 2A

source_name: Tumor 2A


title: Tumor 8A

description: Gene expression data from Tumor 8A

source_name: Tumor 8A


title: Tumor 10A

description: Gene expression data from Tumor 10A

source_name: Tumor 10A


title: Mel DP

description: Gene expression data from Mel DP

source_name: Mel DP

tag: Mel DP


title: Tumor 1302

description: Gene expression data from Tumor 1302

source_name: Tumor 1302


title: Mel LP

description: Gene expression data from Mel LP

source_name: Mel LP

tag: Mel LP


title: Tumor 3B

description: Gene expression data from Tumor 3B

source_name: Tumor 3B


title: Tumor 3629

description: Gene expression data from Tumor 3629

source_name: Tumor 3629


title: Tumor 9166

description: Gene expression data from Tumor 9166

source_name: Tumor 9166


title: Tumor 9B

description: Gene expression data from Tumor 9B

source_name: Tumor 9B


title: Tumor 3A

description: Gene expression data from Tumor 3A

source_name: Tumor 3A


title: Tumor 9141

description: Gene expression data from Tumor 9141

source_name: Tumor 9141


title: Tumor 6B

description: Gene expression data from Tumor 6B

source_name: Tumor 6B


title: Tumor 16A

description: Gene expression data from Tumor 16A

source_name: Tumor 16A


title: Tumor 4479

description: Gene expression data from Tumor 4479

source_name: Tumor 4479


title: Samsung PAO1, rep3

status: Public on Aug 29 2008

city: Fort Collins

first: Tiffany

middle: L

last: Weir

address: 1173 Campus Delivery

institute: Colorado State University

description: Gene expression data from P. aeruginosa recovered from susceptible host tissue

hyb_protocol: Hybridization was conducted by Asuragen Inc. using Affymetrix P. aeruginosa (900339) Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a high-resolution GeneChip 3000 scanner.

data_processing: The data analysis was performed using GeneSpring 7.2 (Silicon Genetics, Redwood City, CA) DNAChip Analyzer (dChip; http://www.dchip.org). The data were normalized per chip by dChip invariant set normalization, and each gene was normalized to the median measurement taken for that gene across all the samples.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa recovered from N. tabacum cv. Samsun

label_protocol: cDNA for microarray was labeled by Asuragen Inc.

growth_protocol: Bacteria were grown overnight in Luria-Bertani broth prior to dilution with 10mM MgSO4. Diluted bacteria were infiltrated into leaves of Nicotana tabacum (5x106 cells/leaf) and incubated overnight at 30C.

extract_protocol: RNA extraction was performed according to the manufacturer's instructions using the Ribopure RNA isolation kits from Ambion Inc .

treatment_protocol: After 24 hours, leaves were reinfiltrated with sdH2O and bacteria were removed from saturated leaves by centrifugation. Collected bacterial pellets were immediately flash frozen in liquid nitrogen and RNA was extracted.

tag: P. aeruginosa recovered from susceptible host tissue, Samsung PAO1


title: Tumor 476

description: Gene expression data from Tumor 476

source_name: Tumor 476


title: Samsung PAO1, rep2


title: Tumor 550

description: Gene expression data from Tumor 550

source_name: Tumor 550


title: Samsung PAO1, rep1

source_name: Pseudomonas aeruginosa recovered from N. tabacum cv. Samaun


title: Tumor 6A

description: Gene expression data from Tumor 6A

source_name: Tumor 6A


title: Tumor 482

description: Gene expression data from Tumor 482

source_name: Tumor 482


title: Xanthi PAO1, rep3

description: Gene expression data from P. aeruginosa recovered from resistant host tissue

source_name: Pseudomonas aeruginosa recovered from N. tabacum cv. Xanthi

tag: P. aeruginosa recovered from resistant host tissue, Xanthi PAO1


title: Xanthi PAO1, rep2


title: Tumor 2B

description: Gene expression data from Tumor 2B

source_name: Tumor 2B


title: Xanthi PAO1, rep1


title: 96 hrs after TPA treatment, biological replicate 2

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: Biological replicate 2 of 3

hyb_protocol: Arrays were hybridized at 60°C for 16 hours in a rotating hybridization oven (Agilent). Arrays were washed with a combination of wash buffers containing SSC and Triton X-102.

scan_protocol: Arrays were scanned using an Axon Instruments GenePix 4000B scanner, and fluorescence was quantified using the GenePix 6.0 software.

data_processing: Raw data were normalized and quantified using limma library, part of the Bioconductor project, using the R statistical environment for Operon arrays. LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal.

source_name: promonocytic cell line U937, TPA treatment for 96 hrs, differentiating cells

label_protocol: Total RNA was reverse-transcribed into double-stranded cDNA using Superscript II (Invitrogen) and a T7 oligo-dT primer, and subsequently amplified using a Megascript T7 protocol (Ambion). cRNA was fluorescently labeled by conjugation with Cy-dyes (Cy3 and Cy5) using Micromax ASAP (Perkin Elmer), and purified using a YM-100 column (Millipore)

growth_protocol: Cells were maintained in RPMI 1640 medium (Mediatech) supplemented with 10% fetalclone (HyClone)

extract_protocol: RNA was extracted using the RNeasy kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: U937 cells were differentiated by the addition to the growth medium 100 nM 12-O-tetradeconoyl-phorbol-13-acetate (TPA)

source_name: promonocytic cell line U937, no TPA treatment, undifferentiated cells


title: 96 hrs after TPA treatment, biological replicate 3

description: Biological replicate 3 of 3

tag: TPA treatment for 96 hrs, differentiating cells

tag: no TPA treatment, undifferentiated cells


title: 27 hrs after TPA treatment, biological replicate 3

description: Biological replicate 3 of 3

source_name: promonocytic cell line U937, TPA treatment for 27 hrs, differentiating cells


title: 27 hrs after TPA treatment, biological replicate 1

description: Biological replicate 1 of 3

tag: TPA treatment for 27 hrs, differentiating cells


title: Tumor 14B

description: Gene expression data from Tumor 14B

source_name: Tumor 14B


title: 27 hrs after TPA treatment, biological replicate 2

description: Biological replicate 2 of 3


title: 96 hrs after TPA treatment, biological replicate 1

description: Biological replicate 1 of 3


title: macaque B cell lymphoma RNA positive for rhesus rhadinovirus

city: Beaverton

first: Scott

middle: William

last: Wong

state: OR

address: 505 NW 185th Avenue

department: Vaccine and Gene Therapy Institute

institute: Oregon Health & Science University

description: Quality assessment was done using BioConductor.

hyb_protocol: Cy5 and Cy3 labeled sample pairs were hybridized to two slides (two arrays per slide) in 5x SSC / 0.1%  SDS with human cot-1 DNA and polyA DNA for 16 hours at 60C.  Cy3 channels for all arrays were the same reference sample.

scan_protocol: Arrays were scanned with a ScanArray 4000 XL microarray scanner (PerkinElmer) at 5 micron resolution.  Images were stored as 16-bit tiff files.

data_processing:
Array images were quantitated using ImaGene (BioDiscovery)
Scalar values from images represent a 2^16 relative range of values.  Matrix values are Cy5 / Cy3 normalized averages of four replicate measures.

organism: Macaca mulatta

source_name: Tumor specific RNA obtained at necropsy

label_protocol: RNA was amplified using the MessageAmp protocol (Ambion).  2.5 micrograms of aRNA was used as template for making amino-allyl cDNA using the CyScribe protocol (PerkinElmer).  Samples were then labeled with Cy5 (Amersham).

growth_protocol: Experimentally infected animals were housed in animal biosafety level 2+ containment.

extract_protocol: Frozen tumor tissue was placed in 1.0 mL of TRI-Reagent and homogenized with a tissue tearor. Total cellular RNA was then processed following the manufacturer's (TRI-Reagent) instructions.

treatment_protocol: Tumor tissue obtained from the animal was flash frozen in liquid nitrogen and stored at -80oC.

tag: B cell (CD20+) lymphoma collected from rhesus macaque that was experimentally infected with simian immunodeficiency virus (SIV) and later with rhesus macaque rhadinovirus (RRV).

source_name: Normal CD20+ B cells

label_protocol: Normal B cell derived RNA and tumor RNA was amplified using the MessageAmp protocol (Ambion).  2.5 micrograms of aRNA was used as template for making amino-allyl cDNA using the CyScribe protocol (PerkinElmer).  Samples were then labeled with Cy3 (Amersham).

growth_protocol: not applicable

extract_protocol: CD20+ B cells were resuspended in TRI-Reagent and RNA purified per the manufacturer's instructions.

treatment_protocol: Peripheral blood mononuclear cells were treated with magnetic beads coated with anti-CD20 monoclonal antibodies. Samples were washed 3x to remove non-bead bound cells.

tag: CD20+ B cells were enriched by magnetic bead selection from peripheral blood mononuclear cells obtained from six different rhesus macaques that were sero-negative for rhesus macaque rhadinovirus.


title: LD 24 (5-0)

city: Camden

first: Kwangwon

last: Lee

address: 315 Penn Street

department: Department of Biology, Center for Computational & Integrative Biology

institute: Rutgers University

description: treatment: LD 24 (5-0)

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with 6x SSC/0.005% Triton X-102 and 0.1x SSC/0.005% Triton X-102 before scanning. Slides were hybridized for 17 h at 60°C in a rotating oven, and washed.

scan_protocol: Scanned on an Agilent scanner. Images were quantified using Agilent Feature Extraction Software

data_processing: background subtracted VALUE data obtained from log of processed Green signal/processed Red signal.

organism: Pyricularia oryzae

source_name: total RNA from sample "LD 24 (5-0)" labeled with Cyanine-3 (green).

label_protocol: Labels were prepared using Agilent Low RNA Input Fluorescent Linear Amplification Kit (5184-3523) following the manufacturer’s recommendations. Briefly, 10 µg of total RNA were extracted. About 500 ng of each RNA sample was used for the first strand synthesis. 1.2 µL of T7 Promoter Primer was used for each reaction. The primer and the template by incubating the reaction at 65°C in a heating block for 10 minutes. The reactions were placed on ice and incubate for 5 minutes, gently mixed the components of the cDNA master mix by pipetting. For cDNA synthesis, samples were incubated at 40°C in a circulating water bath for 2 hours, and then, inactivated MMLV-RT at 65°C for 15 minutes. To each sample tube, EITHER 2.4 µL cyanine 3-CTP (10 mM) or 2.4 µL cyanine 5-CTP (10 mM) was used. 57.6 µL of Transcription Master Mix was mixed by pipetting, and Incubated samples in a circulating water bath at 40°C for 2 hours. cRNAs were purified using Qiagen’s RNeasy mini spin columns.

growth_protocol: Sample were cultured in complete liquid media; for 1 liter, 50 ml 20X nitrate salts, 1ml trace elements, 10g D-glucose, 2g peptone, 1g Yeast Extract, 1g Casamino Acids, 1ml vitamin solution. pH was adjusted to 6.5 with NaOH. 20X Nitrate Salts; for 1L, 120 g NaNO3, 10.4g KCl, 10.4g MgSO47H2O, 30.4g KH2PO4. Trace elements (X1000, for 100 ml); 2.2g ZnSO47H2O, 1.1g H3BO3, 0.5g MnCl24H2O, 0.5g FeSO47H2O, 0.17g CoCl26H2O, 0.16g CuSO45H2O,  0.15g Na2MoO42H2O, 5g Na4EDTA. Vitamin Solution (for 100ml); 0.01g Biotin, 0.01g Pyridoxin, 0.01g Thiamine, 0.01g Riboflavin, 0.01g PABA (p-aminobenzoic acid), 0.01g nicotinic acid. Temperature was maintained at 24 ± 0.5 °C.

extract_protocol: TriZol procedure

tag: Strain

value: mycelia

tag: Age

value: one day old

tag: Light culture condition

value: 24 hour in darkness after light-to-dark transition

tag: replicate #1

source_name: pooled RNA from all samples, labeled with Cyanine-5 (red).


title: LD 2 (3-0)

description: treatment: LD 2 (3-0)

source_name: total RNA from sample "LD 2 (3-0)" labeled with Cyanine-3 (green).

tag: Tissue

value: 2 hour in darkness after light-to-dark transition


title: Tumor 243

description: Gene expression data from Tumor 243

source_name: Tumor 243


title: LD 2 (3-1)

description: treatment: LD 2 (3-1)

source_name: total RNA from sample "LD 2 (3-1)" labeled with Cyanine-3 (green).

tag: replicate #2


title: LD 12 (4-1)

description: treatment: LD 12 (4-1)

source_name: total RNA from sample "LD 12 (4-1)" labeled with Cyanine-3 (green).

value: 12 hour in darkness after light-to-dark transition


title: LL (1-1)

description: treatment: LL (1-1)

source_name: total RNA from sample "LL (1-1)" labeled with Cyanine-3 (green).

value: constant light 24 hour


title: LD 12 (4-0)

description: treatment: LD 12 (4-0)

source_name: total RNA from sample "LD 12 (4-0)" labeled with Cyanine-3 (green).


title: LD 24 (5-2)

description: treatment: LD 24 (5-2)

source_name: total RNA from sample "LD 24 (5-2)" labeled with Cyanine-3 (green).

tag: replicate #3


title: LD 2 (3-2)

description: treatment: LD 2 (3-2)

source_name: total RNA from sample "LD 2 (3-2)" labeled with Cyanine-3 (green).


title: LL (1-0)

description: treatment: LL (1-0)

source_name: total RNA from sample "LL (1-0)" labeled with Cyanine-3 (green).


title: LL (1-2)

description: treatment: LL (1-2)

source_name: total RNA from sample "LL (1-2)" labeled with Cyanine-3 (green).


title: LD 12 (4-2)

description: treatment: LD 12 (4-2)

source_name: total RNA from sample "LD 12 (4-2)" labeled with Cyanine-3 (green).

tag: Due to the low Cy5 signal intensities, data from this sample was removed from the analysis.


title: LD 0.5 (2-0)

description: treatment: LD 0.5 (2-0)

source_name: total RNA from sample "LD 0.5 (2-0)" labeled with Cyanine-3 (green).

value: 30 min in darkness after light-to-dark transition


title: LD 24 (5-1)

description: treatment: LD 24 (5-1)

source_name: total RNA from sample "LD 24 (5-1)" labeled with Cyanine-3 (green).


title: Ovarian cancer cell line ES-2

type: genomic

city: London

first: Ken

last: Choi

address: 46 Cleveland Street

department: Gynaecological Oncology

country: United Kingdom

institute: University College London

hyb_protocol: Test and reference DNA samples (50μl each) were combined, precipitated together with 100μg of human Cot1 DNA (1μg/μl, Invitrogen) and resuspended in 100μl of hybridization buffer (50% formamide, 10% dextran sulphate, 2X SSC, 2% SDS, 4μg/μl yeast tRNA). The samples were denatured at 70oC for 15mins and pre-hybridized at 37oC for 60mins. Meanwhile, array slides were denatured at 95oC for 2mins, allowed to cool and pre-hybridized in blocking buffer (25% formamide, 0.1% SDS, 5X SSC, 1g BSA) at 42oC for 60mins. The array slides were gently washed in 0.1X SSC for 30secs and spun dry at 2000rpm for 3mins. The pre-hybridized test and reference DNA samples were applied onto cover slips and hybridized onto the array slides. The slides were then transferred into a small hybridization chamber containing Whatmann 3MM paper saturated with dH20 and incubated in a rocking hybridization oven at 42oC for 24hrs. Post hybridization, slides were washed in 2X SSC, 0.1% SDS at 45oC for 15mins, then 2X SSC, 50% formamide at 45oC for 15mins, then 2X SSC, 0.1% SDS at 45oC for 30mins and finally followed by 0.2X SSC for 15mins at room temperature. Slides were spun dry in a centrifuge for 3mins at 2000rpm and stored in a dark dry container until scanning.

scan_protocol: Hybridized microarrays were scanned using an Axon GenePix 4000B scanner at 5micron scans for both channels.

data_processing: Images were put through a data extraction program called BlueFuse (Blue Gnome, Cambridge UK) along with a clone position file. Primary data analysis and normalisation were carried out using web-based analysis tool called LIMS (Laboratory Information Management System) developed in our laboratory. The microarray data were normalised using lowess and MANOR algorithms and data points smoothed using a 1Mb window.

molecule: genomic DNA

source_name: Cell line DNA ES-2

label_protocol: Invitrogen: Genomic Bioprime Total kit

extract_protocol: Qiagen DNA mini kit

tag: Genomic amplified DNA

source_name: Genomic DNA normal female


title: LD 0.5 (2-1)

description: treatment: LD 0.5 (2-1)

source_name: total RNA from sample "LD 0.5 (2-1)" labeled with Cyanine-3 (green).


title: Ovarian cancer cell line IGROV-1

source_name: Cell line DNA IGROV-1


title: Ovarian cancer cell line SW626

source_name: Cell line DNA SW626


title: Ovarian cancer cell line HX/62

source_name: Cell line DNA HX/62


title: Ovarian cancer cell line OVCA-X

source_name: Cell line DNA OVCA-X


title: Ovarian cancer cell line CAOV-3

source_name: Cell line DNA CAOV-3


title: Ovarian cancer cell line OAW42

source_name: Cell line DNA OAW42


title: H3K4me3 location in U937 cells, average of three biological replicates

description: H3K4me3 location in U937 cells (biolgical rep1, 2 and 3)

hyb_protocol: Hybridization was performed in 25% formamide/5X SSC/0.1% SDS/2 mg/ml BSA/0.3 mg/ml Cot-1 DNA/0.6 mg/ml yeast tRNA in the 50C water-tight hybridization chamber (Corning) for 16 hours. The following day, hybridization chambers were disassembled, the coverslips were removed, and the slides were immediately placed in 2X SSC and 0.1% SDS at room temperature for 5 min at 50C with agitation. The slides were then transferred to 0.1X SSC/0.1% SDS at room temperature for 10 min with agitation. The slides were then transferred to 0.1X SSC for 1 min at room temperature with agitation. This step was repeated two more times. The slides were placed in a rack and dried by centrifugation (Eppendorf centrifuge 5804) for 2 min at 1000 rpm and were immediately scanned or stored in the dark.

scan_protocol: Arrays were scanned using an Axon Instruments GenePix 4000B scanner.

data_processing:
Normalization was performed as described (Boyer et al., 2005). In particular, the array includes a set of negative control spots which sequences that do not cross-hybridize to human genomic DNA. We calculated the median intensity of these negative control spots in each channel and then subtracted this number from the intensities of all other features. To correct for different amounts of input DNA and immunoprecipitated (IP) DNA hybridized to the chip, the negative control-subtracted median intensity value of the IP DNA channel was then divided by the median of the input DNA channel. This yielded a normalization factor that was applied to each intensity value in the input DNA channel. From the normalized intensity values obtained from three biological replicates (from 1 to 3) for each probe, average intensity value for each probe was defined. The ratio of the intensity value in IP (normalized) to the intensity value in input (normalized) describes binding ratio. Next, we calculated the log of the ratio of intensity in the IP channel to intensity in the input channel for each probe. Average log ratio over three replicates with propagation error were obtained and used in a whole chip error model (Hughes et al., 2000) to calculate confidence values for each spot (p-value). This error model functions by converting the intensity information in both channels to an X score which is dependent on both the absolute value of intensities and background noise in each channel using an f-score as described (Boyer et al., 2005). The X scores for an array are assumed to be normally distributed which allows for calculation of a p-value for the enrichment ratio seen at each feature.
A whole-chip error model was used to calculate confidence values (p-values) for each spot on the array

source_name: promonocytic cell line U937, chromatin immunoprecipitation using H3K4me3 antibodies ab8580

label_protocol: Amplified PCR product was used as template for a random-primed, Klenow-based extension reaction using the Bioprime Array CGH Labeling Module (Invitrogen), incorporating a Cy5- or Cy3-dUTP to yield fluorescently-labeled DNA for hybridization.

extract_protocol: Chromatin was isolated and immunoprecipitated (ChIP) following established protocols. After the ChIP, recovered DNA was amplified by LM-PCR.

source_name: promonocytic cell line U937, input DNA


title: LD 0.5 (2-2)

description: treatment: LD 0.5 (2-2)

source_name: total RNA from sample "LD 0.5 (2-2)" labeled with Cyanine-3 (green).

source_name: pooled RNA from all samples, labeled with Cyanine-5 (red).


title: Ovarian cancer cell line OAW59M

source_name: Cell line DNA OAW59M


title: Ovarian cancer cell line COV-413

source_name: Cell line DNA COV-413


title: Ovarian cancer cell line PNX94

source_name: Cell line DNA PNX94


title: Ovarian cancer cell line COV-362.4

source_name: Cell line DNA COV-362.4


title: Ovarian cancer cell line PEO-14

source_name: Cell line DNA PEO-14


title: Ovarian cancer cell line SKOV-3

source_name: Cell line DNA SKOV-3

source_name: Genomic DNA normal female


title: Ovarian cancer cell line COV-434

source_name: Cell line DNA COV-434


title: Ovarian cancer cell line 1847

source_name: Cell line DNA 1847


title: Conjunctival_clone3

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix Porcine genome arrays were hybridized with 11 mg of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Sus scrofa

source_name: Conjunctival keratinocyte clone from biopsy

label_protocol: 1 micro-gramme of total RNA were amplified and labeled using Affymetrix eukaryotic taget preparation (one-cycle amplification, #701025 Rev.2)

growth_protocol: Biopsies of conjunctiva or cornea taken at distance (6mm) from the limbus were obtained from white domestic pigs (AP1 and AP6) soon after sacrifice. Biopsies were dissociated using 0.05 % trypsin in 0.01% EDTA and the keratinocytes cultivated on a feeder layer of irradiated 3T3-J2 cells in a 3:1 DMEM F12 medium supplemented as described (Oshima et al., Cell 2001). Single cells were isolated after the mass cultures with an elongated Pasteur pipet under an inverted microscope as described (Barrandon and Green Proc Natl Acad Sci USA, 1985) and cultivated as above.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN Inc.)

tag: Passage V conjunctival keratinocyte clone

tag: Generates goblet cells in culture

tag: Expresses stem cell markers (p63, Zfp145, Bmi1), marker of corneal differentiation (K12) and of conjunctival differentiation (Muc5ac, K4 and K19)


title: Conjunctival_clone1


title: Ovarian cancer cell line OVCAR-10

source_name: Cell line DNA OVCAR-10


title: Ovarian cancer cell line TOV21G

source_name: Cell line DNA TOV21G


title: Central_Corneal_clone3

source_name: Corneal keratinocyte clone from biopsy

tag: Passage V corneal keratinocyte clone


title: Ovarian cancer cell line JAMA-2

source_name: Cell line DNA JAMA-2


title: Ovarian cancer cell line 1847AD

source_name: Cell line DNA 1847AD


title: Central_Corneal_clone2


title: Conjunctival_clone2


title: Ovarian cancer cell line TOV112D

source_name: Cell line DNA TOV112D


title: Ovarian cancer cell line LK1

source_name: Cell line DNA LK1


title: Ovarian cancer cell line COV-318

source_name: Cell line DNA COV-318


title: Ovarian cancer cell line TRL-12B

source_name: Cell line DNA TRL-12B


title: Central_Corneal_clone1


title: Ovarian cancer cell line TRL-90T

source_name: Cell line DNA OV-TRL-90T


title: Ovarian cancer cell line OVCAR3

source_name: Cell line DNA OVCAR3


title: Ovarian cancer cell line COV644

source_name: Cell line DNA COV-644


title: Ovarian cancer cell line LK2

source_name: Cell line DNA LK2


title: Ovarian cancer cell line OVMZ15

source_name: Cell line DNA OV-MZ-15

source_name: Genomic DNA normal female


title: Ovarian cancer cell line Intov2

source_name: Cell line DNA INTOV2


title: Ovarian cancer cell line OAW41M

source_name: Cell line DNA OAW41M


title: no TPA treatment, average of three biological replicates

hyb_protocol: Hybridization was performed in 25% formamide/5X SSC/0.1% SDS/2 mg/ml BSA/0.3 mg/ml Cot-1 DNA/0.6 mg/ml yeast tRNA. in the 50C water-tight hybridization chamber (Corning) for 16 hours. The following day, hybridization chambers were disassembled, the coverslips were removed, and the slides were immediately placed in 2X SSC and 0.1% SDS at room temperature for 5 min at 50C with agitation. The slides were then transferred to 0.1X SSC/0.1% SDS at room temperature for 10 min with agitation. The slides were then transferred to 0.1X SSC for 1 min at room temperature with agitation. This step was repeated two more times. The slides were placed in a rack and dried by centrifugation (Eppendorf centrifuge 5804) for 2 min at 1000 rpm and were immediately scanned or stored in the dark.

source_name: promonocytic cell line U937, no TPA treatment, undifferentiated cells, IP DNA

growth_protocol: SAOS-2 human osteosarcoma cells were grown in DMEM medium (Mediatech) supplemented with 10% fetal bovine serum (FBS). U937 human promonocytic cells were maintained in RPMI 1640 medium (Mediatech) supplemented with 10% fetalclone (HyClone)

extract_protocol: Chromatin was isolated and immunoprecipitated (ChIP) with affinity-purified rabbit RBP2 antibodies 1416 following established protocols. After the ChIP, recovered DNA was amplified by LM-PCR.

source_name: promonocytic cell line U937, no TPA treatment, undifferentiated cells input DNA


title: 27 hrs after TPA treatment, average of three biological replicates

source_name: promonocytic cell line U937, TPA treatment for 27 hrs, differentiating cells, IP DNA

source_name: promonocytic cell line U937, TPA treatment for 27 hrs, differentiating cells, input DNA


title: 96 hrs after TPA treatment, average of three biological replicates

source_name: promonocytic cell line U937, TPA treatment for 96 hrs, differentiating cells, IP DNA

source_name: promonocytic cell line U937, TPA treatment for 96 hrs, differentiating cells, input DNA


title: unrelated cell line, average of three biological replicates

source_name: osteosarcoma cell line SAOS-2, untreated, IP DNA

tag: unrelated cell line

source_name: promonocytic cell line U937, unrelated cell line,input DNA


title: Ovarian cancer cell line OVP1

source_name: Cell line DNA OVP1


title: Primary CMV infection: naive CD8+, dye swap

status: Public on Aug 28 2008

city: Amsterdam

first: Amber

last: van Stijn

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Academic Medical Center

hyb_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

data_processing: The default Agilent normalization procedure, called Linear & Lowess, was applied.Exact protocol and parameter settings are described in the Agilent Feature Extraction Software User Manual 7.5 (http://chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=37629).

source_name: CD8+ T cells, naive

label_protocol: Dye Coupling Reaction (Amersham, England)

growth_protocol: ex vivo isolated CD8+ T cells

extract_protocol: nucleospin RNA isolation kit (Machery-Nagel, Düren, Germany)

tag: Stage

value: naïve

tag: Type

value: CD45RA+CD27+CD8+ cells


title: Primary CMV infection: peak, dye swap

description: Primary CMV infection: peak, dye swap

scan_protocol: Agilent Technologies (Santa Clara, CA) following manufacturer’s protocol.

source_name: CD8+ T cells, peak

value: peak


title: Primary CMV infection: latent, dye swap

description: Primary CMV infection: latent, dye swap

source_name: CD8+ T cells, latent

value: latent

value: pp65-CMV-specific tetramer+ CD8+ cells


title: Primary CMV infection: naive CD8+

description: Primary CMV infection: naive CD8+


title: Primary CMV infection: 1 year p.i., dye swap

source_name: CD8+ T cells, 1 year p.i.

value: 1 year p.i


title: PrP-null KO 30 days post-Dox 1

status: Public on Aug 27 2008

city: Winnipeg

first: Debra

last: Parchaliuk

state: Manitoba

address: 1015 Arlington Street

department: Prion Diseases Program

country: Canada

institute: Public Health Agency of Canada

description: Uninfected aged-matched mice used as control

hyb_protocol: A total of 16,315 cDNA expressed sequence tags were spotted in duplicate onto CMT-GAPS Gamma Amino Propyl Silane coated glass slides (Corning) using the Virtek Chip Writer. 5ug of both reference (WT) and experimental (KO and HQK) Alexa Flour labeled aRNA were used in each competitive hybridization. Each labeled aRNA was resuspended in 35ml DIG Easy HybTM hybridization buffer (Roche) containing 20mg mouse cot1 DNA and 20 mg poly(A)-DNA to block non-specific hybridization. Three biological replicate samples from each of the reference and experimental groups were combined, heated for 5 minutes at 95°C, then cooled and maintained at 42°C. The labeled aRNA sample mixtures were added to a BMAP-MSV microarray and incubated in the dark at 42°C overnight to competitively hybridize to reference and experimental samples. The number of slides hybridized in each experiment corresponded to the number of biological replicates in each group of experimental interest. Following hybridization, the slides were washed once in low stringency wash buffer (1X SSC, 0.2% SDS) preheated to 42°C for 5 minutes, once in high stringency wash buffer (0.1X SSC, and 0.2%SDS) for 5 minutes at room temperature, and then once in 0.1X SSC for 5 minutes at room temperature.

scan_protocol: The slides were analyzed in two channels using the Agilent HT microarray scanner (Agilent).

data_processing: Raw, background and net intensity values were collected using Array-Pro software (MediaCybernetics). In order to account for variation in fluorescence, LOWESS sub-grid normalization was performed by Gene Traffic software (Iobion), and the subsequent normalized log2 ratios obtained.

label: AlexaFluor 555

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications.  In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis.  In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified.  10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 555 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour.  Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

extract_protocol: Total RNA was isolated from frozen skeletal muscle using the Qiagen RNeasy skeletal muscle RNA isolation kit (Qiagen) following manufacturers’ specifications.  The total RNA preparations were further treated with Turbo DNA-Free DNase (Ambion) to remove residual genomic DNA contamination, and examined with an Agilent 2100 Bioanalyzer (Agilent) for purity and quantity.

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

tag: Line

value: Wild-type

tag: Treatment

value: 30 days post Dox admin

label: AlexaFluor 647

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications. In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis. In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified. 10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 647 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour. Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

tag: Line:PrP-null (KO) mice


title: Primary CMV infection: latent

description: Primary CMV infection: latent


title: PrP overexpression HQK-3 30 days post-Dox

extract_protocol: Total RNA was isolated from frozen skeletal muscle using the Qiagen RNeasy skeletal muscle RNA isolation kit (Qiagen) following manufacturers’ specifications. The total RNA preparations were further treated with Turbo DNA-Free DNase (Ambion) to remove residual genomic DNA contamination, and examined with an Agilent 2100 Bioanalyzer (Agilent) for purity and quantity.

treatment_protocol: Transgenic HQK mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: Transgenic HQK

value: 30 days after Dox admin


title: Primary CMV infection: peak

description: Primary CMV infection: peak


title: PrP-null KO 30 days post-Dox 3 DS

hyb_protocol: A total of 16,315 cDNA expressed sequence tags were spotted in duplicate onto CMT-GAPS Gamma Amino Propyl Silane coated glass slides (Corning) using the Virtek Chip Writer.   5ug of both reference (WT) and experimental (KO and HQK) Alexa Flour labeled aRNA were used in each competitive hybridization.   Each labeled aRNA was resuspended in 35ml DIG Easy HybTM hybridization buffer (Roche) containing 20mg mouse cot1 DNA and 20 mg poly(A)-DNA to block non-specific hybridization.   Three biological replicate samples from each of the reference and experimental groups were combined, heated for 5 minutes at 95°C, then cooled and maintained at 42°C.  The labeled aRNA sample mixtures were added to a BMAP-MSV microarray and incubated in the dark at 42°C overnight to competitively hybridize to reference and experimental samples. The number of slides hybridized in each experiment corresponded to the number of biological replicates in each group of experimental interest.  Following hybridization, the slides were washed once in low stringency wash buffer (1X SSC, 0.2% SDS) preheated to 42°C for 5 minutes, once in high stringency wash buffer (0.1X SSC, and 0.2%SDS) for 5 minutes at room temperature, and then once in 0.1X SSC for 5 minutes at room temperature.

tag: Line:PrP-null (KO)

label_protocol: Total RNA was amplified and labeled for microarray analysis using the AminoAllyl Message Amp II aRNA amplification kit (Ambion) following manufacturers specifications.  In brief, 1ug total RNA was reverse transcribed to first-strand cDNA, followed by subsequent second-strand cDNA synthesis.  In vitro transcription to synthesize amplified aRNA was performed and the resultant aRNA quantified.  10-15ug aRNA was coupled to Alexa Fluor succinimidyl ester 647 dye in 30% DMSO/coupling buffer in the dark at room temperature for 1 hour.  Uncoupled dyes were removed and labeled aRNA purified following manufacturers’ specifications.


title: Primary CMV infection: 1 year p.i.

description: Primary CMV infection: 1 year p.i.

source_name: CD8+ T cells, 1 year p.i


title: 3-22-05_time_course_part2_MYC_reactivate_12hr

last: Stanford Microarray Database

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60419.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 12 h

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.04; Parameter Scan Time = 15:20:20; Parameter PMT Volts = 580; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210881; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.04; Parameter Scan Time = 15:20:20; Parameter PMT Volts = 610; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575685; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm), default computed normalization procedure, see SMD website

source_name: mouse common reference

label_protocol: not provided

extract_protocol: not provided

tag: mouse common reference

source_name: 1325 +dox for 48 hr then remove for 12hr


title: 3-22-05_time_course_part2_MYC_reactivate_18hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60420.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 18 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.15; Parameter Scan Time = 15:39:16; Parameter PMT Volts = 580; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210901; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.15; Parameter Scan Time = 15:39:16; Parameter PMT Volts = 640; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575705; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 18hr


title: 2-15-05_time_course_part_one_+dox_3.5hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59302.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 3.5 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1120, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.58; Parameter Scan Time = 11:43:34; Parameter PMT Volts = 580; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203080; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.45; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.58; Parameter Scan Time = 11:43:34; Parameter PMT Volts = 630; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567884; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.98; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: reference 30ug

tag: reference 30ug

source_name: 1325 + dox for 3.5 hr

tag: 1325 + dox for 3.5 hr


title: PrP-null KO 30 days post-Dox 2


title: 3-22-05_time_course_part2_MYC_reactivate_36hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60422.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 36 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5840; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.30; Parameter Scan Time = 16:11:35; Parameter PMT Volts = 600; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210932; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.38; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.30; Parameter Scan Time = 16:11:35; Parameter PMT Volts = 660; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575736; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.10; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 36hr


title: PrP overexpression HQK-3 7 days post-Dox DS

treatment_protocol: Transgenic Tg(HQK) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: 7 days after Dox admin

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: Wild-Type


title: 3-22-05_time_course_part2_MYC_reactivate_24hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60421.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 24 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5480; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.22; Parameter Scan Time = 15:54:41; Parameter PMT Volts = 590; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210917; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.22; Parameter Scan Time = 15:54:41; Parameter PMT Volts = 630; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575720; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.12; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 24hr


title: PrP-null KO 30 days post-Dox 2 DS


title: 2-15-05_time_course_part_one_+dox_24hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59306.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 24 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.62; Parameter Scan Time = 10:08:41; Parameter PMT Volts = 560; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 202986; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.62; Parameter Scan Time = 10:08:41; Parameter PMT Volts = 620; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567790; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.93; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 + dox for 24hr

tag: 1325 + dox for 24hr


title: PrP-null KO 14 days post-Dox 3 DS

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

value: 14 days post Dox admin

treatment_protocol: Wild Type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 14 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: 3-22-05_time_course_part2_MYC_reactivate_8hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60418.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 8 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5000; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.94; Parameter Scan Time = 15:05:21; Parameter PMT Volts = 570; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210867; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.94; Parameter Scan Time = 15:05:21; Parameter PMT Volts = 640; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575671; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.06; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 8 hr


title: 2-15-05_time_course_part_one_+dox_11.5hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59304.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 11.5 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.23; Parameter Scan Time = 11:06:16; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203042; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.46; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.23; Parameter Scan Time = 11:06:16; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567846; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.94; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu


title: 3-22-05_time_course_part1_+dox48hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60416.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 48 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.81; Parameter Scan Time = 14:47:21; Parameter PMT Volts = 550; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210850; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.81; Parameter Scan Time = 14:47:21; Parameter PMT Volts = 720; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575653; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.01; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 + dox for 48hr

tag: 1325 + dox for 48hr


title: PrP-null KO 7 days post-Dox 2

value: 7 days post Dox admin

treatment_protocol: PrP-null (KO) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 7 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: 3-22-05_time_course_part2_MYC_reactivate_48hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60423.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 48 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 1360, 5320; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.38; Parameter Scan Time = 16:26:53; Parameter PMT Volts = 580; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210948; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 40.38; Parameter Scan Time = 16:26:53; Parameter PMT Volts = 650; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575752; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.09; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 48hr


title: 2-15-05_time_course_part_one_+dox_48hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59308.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 48 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.96; Parameter Scan Time = 10:37:22; Parameter PMT Volts = 570; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203014; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.44; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.96; Parameter Scan Time = 10:37:22; Parameter PMT Volts = 610; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567818; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.92; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu


title: 3-22-05_time_course_part2_MYC_reactivate_4hr

description:
Simple annotation: myc, tetracycline induction
Image: http://smd.stanford.edu/MicroArray/gifs/2005-03/60417.gif
Measurement: concentration(absolute) 0 other
Measurement: time(relative) 4 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 800, 4800; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 14:15:29; Parameter PMT Volts = 570; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 210817; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.63; Parameter Scan Time = 14:15:29; Parameter PMT Volts = 690; Parameter Scan Date = 2005-03-22; Parameter Pixel Size = 10; Parameter Laser on time = 575621; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 2.03; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 +dox for 48 hr then remove for 4 hr


title: PrP overexpression HQK-1 30 days post-Dox

treatment_protocol: Wild type (WT) mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.

treatment_protocol: HQK transgenic mice were fed food pellets either lacking or containing 6g doxycycline (Dox)/kg food to induce PrPC expression. Skeletal muscles from the quadriceps of hind legs were removed at day 30 days following administration of Dox. The subsequent tissues were used for total RNA extraction.


title: 2-15-05_time_course_part_one_+dox_18hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59305.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 18 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.40; Parameter Scan Time = 09:48:24; Parameter PMT Volts = 590; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 202964; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.43; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 38.40; Parameter Scan Time = 09:48:24; Parameter PMT Volts = 660; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567768; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.88; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 + dox for 18hr

tag: 1325 + dox for 18hr


title: 2-15-05_time_course_part_one_+dox_7.5hr

description:
Simple annotation: myc, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2005-02/59303.gif
Measurement: concentration(absolute) 20 other
Measurement: time(relative) 7.5 h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 960, 5160; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Natalie,,Wu Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.37; Parameter Scan Time = 11:22:14; Parameter PMT Volts = 580; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 203059; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.40; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.3; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 39.37; Parameter Scan Time = 11:22:14; Parameter PMT Volts = 640; Parameter Scan Date = 2005-02-15; Parameter Pixel Size = 10; Parameter Laser on time = 567862; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000A [47263]; Parameter Laser Power = 1.99; Parameter Scanning software version = 2.0.2.3; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Natalie,,Wu

source_name: 1325 + dox for 7.5 hr

tag: 1325 + dox for 7.5 hr


title: PrP overexpression HQK-1 30 days post-Dox DS